Abstract
BackgroundThe phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level.ResultsThe local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range.ConclusionLarge-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.
Highlights
The phylogenetic distribution of large-scale genome structure has been explored mainly by analytical ultracentrifugation of bulk DNA
Isochores - long (>>300 kb), compositionally fairly homogeneous genome regions of different average GC levels were uncovered by analytical ultracentrifugation of bulk DNA [4,5,6,7,8,9,10]
The paradox between a fractal or an isochore structure for the genome has been recently solved in the human genome by the discovery that correlations can show deviations from the power-law behavior [18]. Such deviations can be associated to isochore-like regions [19] -long-homogeneous genome regions computationally predicted by directly examining the genome sequence and sharing many compositional and biological features with true isochores [20,21,22,23,24]
Summary
The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. The paradox between a fractal (scale-invariant) or an isochore structure for the genome has been recently solved in the human genome by the discovery that correlations can show deviations from the power-law behavior [18]. Such deviations can be associated to isochore-like regions [19] -long-homogeneous genome regions computationally predicted by directly examining the genome sequence and sharing many compositional and biological features with true isochores [20,21,22,23,24]
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